Whole bunch of tools are freely available online, which includes QMEAN, What Check, Verify 3D, ModEval, ModFold, MolProbity, ProSA, ProQ, PROCHECK, CASP, CAMEO to name a few.

Dear Ankush,

Please find the attachment. It may solve your query.

All the best

Hi,

To validate your modeled protein structure you can try PDBsum and other tools mentioned above.Hope this helps.

Regards

Dear Ankush,

You can try Structure Analysis and Verification Server (SAVES)  (http://nihserver.mbi.ucla.edu/SAVES), which has inbuilt tools such as PROCHECK, WHAT_CHEK, ERRAT, VERIFY_3D, and PROVE for evaluation of protein 3D model.

With regards

Thank you for valuable suggestion....Thank you Lalit for Review article...

i agree with rajesh kumar pathak

http://bip.weizmann.ac.il/toolbox/structure/validation.htm

go through the link and you will get the useful info..

The best and most important of all the methods for evaluating a protein model is Ramachandran Plot. You can take help from SAVES server http://services.mbi.ucla.edu/SAVES/. Hope this helps, if you could explain more specifically, maybe you can get a more directed answer. 

I don’t have a copy at hand, but this following contains some useful ideas, I think: http://pubs.acs.org/doi/abs/10.1021/pr0155228

Studies in the Assessment of Folding Quality for Protein Modeling and Structure Prediction,  Barry Robson,Tiziana Mordasini and Alessandro Curioni, IBM Research,

Journal of Proteome Research, 2002, 1 (2), pp 115–133

A diagnostic for assessing the quality of a fold has been developed to which further criteria can be progressively added. The goal is to create a measure that can follow the status of a protein structure in a simulation or modeling process, when the answer (the experimental structure) is not known in advance, rather than simply reject deliberate misfolds. This places greater emphasis on the need to study, and calibrate against, marginal cases, i.e., unusual native structures, incomplete structures, partially erroneous X-ray structures, good models, poor models, and the effect of cofactors. The first three terms introduced in the diagnostic are appropriate core-forming properties or noncore properties of residues in relation to tertiary structure, appropriate neighboring structure density for each residue in relation to tertiary structure, and secondary structure consistency. While the method emerges as a useful simulation analysis tool, we find a need for further fine-tuning to diminish sensitivity to minor conformational changes that retain essential features of the fold, balanced against the need to obtain a more sensitive response when a conformational change involves less physically meaningful interatomic interactions. This dual utility is difficult to obtain:  the investigation highlights some of the issues. Initial attempts to obtain it have led to terms in the diagnostic that are admittedly complex:  simplifications must also be explored.

Hi, you can use a web-tool RAMPAGE. You can found it at this link:

http://mordred.bioc.cam.ac.uk/~rapper/rampage.php

It is a very useful!.

Sincerely

Simone

Thank You Barry sir....i ll go through link.....

Hi! we usually use: PROCHECK (www.ebi.ac.uk/thornton-srv/software/PROCHECK/), MolProbity (http://molprobity.biochem.duke.edu/), Verify3D (Structure Evaluation Server - http://services.mbi.ucla.edu/Verify_3D/)...

Thank you Pavel...i ll try

You can use Prosa analysis tool, Phyre2 server and Structure Analysis and Verification Server (SAVES) (http://nihserver.mbi.ucla.edu/SAVES), which encompasses PROCHECK, WHAT_CHEK, ERRAT, VERIFY_3D, and PROVE for evaluation of protein 3D model.

SAVE of NIH server is best for protein model validation cause it provide various programs like ERRAT, PROVE, PROCHECK, WHAT_CHEK, and VERIFY_3D for evaluation of protein structure evaluation.

I have evaluated 3 D structure using different tools. Please check attached file and help me to select best model out of given one.

You need to use Model Quality Assessment Methods (MQAPs), such as ProQ3 -(http://proq3.bioinfo.se/) and ModFOLD4 -(http://www.reading.ac.uk/bioinf/ModFOLD/ModFOLD_form_4_0.html). These programs will give you information on what areas of the model you can trust and use in further studies, in addition to which areas of the model you cannot trust.

Maybe you should have a read of this informative information on model building and assessment -

http://www.proteinmodelportal.org/?pid=101